[gmx-users] PMF using umbrella sampling

[Bob Johnson]

Can you use runtype=constraint in parallel? I switched to using
runtype=umbrella because I received error messages that the
constraints can't be run in parallel.

Also...yes...I switched up angstroms and nanometers...I don't know how
many times I've made that mistake and couldn't find it myself...

Thanks,
Bob

On Tue, Sep 1, 2009 at 2:34 AM, Berk Hess<gmx3 at hotmail.com> wrote:
> Hi,
>
> Firstly, you are not constraining (runtype=constraint), but using a harmonic
> umbrella potential.
>
> Secondly, your distance of 28.9 nm seems enormous, maybe you mixed
> up nanometers and Angstroms here?
>
> Thirdly, I would strongly suggest to switch to Gromacs 4.0.5.
> I have completely rewritten the pull code for Gromacs 4
> and things now work much easier and better.
>
> Berk
>
>> Date: Mon, 31 Aug 2009 12:18:06 -0500
>> From: bobjohnson1981 at gmail.com
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] PMF using umbrella sampling
>>
>> Hello everyone,
>> I'm trying to compute the PMF for pulling two proteins apart. I'm
>> planning on setting up several runs where the COM separation of the
>> proteins is constrained and the constraint force is measured over the
>> course of a long simulation. However, I'm having trouble doing this
>> because I'm unsure of the inputs in the .ppa file. I'm trying to do
>> this with Gromacs 3.3.3. Here is the .ppa file I'm using:
>>
>> runtype = umbrella
>> ngroups = 1
>> reference_group = knob
>> reftype = com
>> pulldim = Y Y Y
>> group_1 = car
>> k1 = 1000
>> pos1 = 0.0 0.0 28.8989219666
>>
>> Here, there are two proteins: car and knob. The COM of car is located
>> at (0.0 0.0 28.8989219666) relative to knob. The problem I'm
>> experiencing is that the simulation results in the two proteins being
>> pulled apart instead of constrained at distance pos1. I believe that
>> I'm misinterpreting the inputs. Does anyone know the solution?
>> Thanks,
>> Bob
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-- 
Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://www.sas.upenn.edu/~robertjo